Starting phenix.real_space_refine on Sun Jun 8 18:00:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.map" model { file = "/net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o38_70072/06_2025/9o38_70072.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6294 2.51 5 N 1674 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9824 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1954 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 400 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1859 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain breaks: 1 Time building chain proxies: 7.29, per 1000 atoms: 0.74 Number of scatterers: 9824 At special positions: 0 Unit cell: (92.176, 97.937, 130.857, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1784 8.00 N 1674 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 53.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 7 through 35 removed outlier: 3.610A pdb=" N VAL B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.695A pdb=" N ILE B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.605A pdb=" N GLN B 102 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 105 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP B 106 " --> pdb=" O CYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 149 through 160 Processing helix chain 'B' and resid 163 through 168 removed outlier: 4.276A pdb=" N TYR B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.712A pdb=" N ALA B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 187 through 209 removed outlier: 4.124A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.594A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.739A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.663A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 601 through 617 removed outlier: 3.537A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.644A pdb=" N TYR A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.018A pdb=" N GLN A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.782A pdb=" N MET A 682 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 683 " --> pdb=" O TYR A 679 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.775A pdb=" N PHE A 730 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.095A pdb=" N SER A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.670A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 819 through 822 Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'F' and resid 567 through 593 Processing helix chain 'F' and resid 596 through 602 Processing helix chain 'F' and resid 604 through 621 removed outlier: 3.545A pdb=" N CYS F 608 " --> pdb=" O GLY F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 624 No H-bonds generated for 'chain 'F' and resid 622 through 624' Processing helix chain 'F' and resid 629 through 663 removed outlier: 5.270A pdb=" N GLN F 637 " --> pdb=" O CYS F 633 " (cutoff:3.500A) Proline residue: F 638 - end of helix Proline residue: F 643 - end of helix Processing helix chain 'F' and resid 665 through 677 removed outlier: 4.220A pdb=" N ARG F 671 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 675 " --> pdb=" O ARG F 671 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG F 677 " --> pdb=" O SER F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 703 Processing helix chain 'F' and resid 728 through 749 removed outlier: 4.473A pdb=" N THR F 736 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN F 737 " --> pdb=" O ALA F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 785 Proline residue: F 780 - end of helix Processing helix chain 'F' and resid 786 through 788 No H-bonds generated for 'chain 'F' and resid 786 through 788' Processing helix chain 'F' and resid 789 through 819 removed outlier: 4.828A pdb=" N LEU F 811 " --> pdb=" O ALA F 807 " (cutoff:3.500A) Proline residue: F 812 - end of helix removed outlier: 3.637A pdb=" N LEU F 816 " --> pdb=" O PRO F 812 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 824 removed outlier: 3.994A pdb=" N LEU F 823 " --> pdb=" O GLN F 820 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN F 824 " --> pdb=" O PRO F 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 820 through 824' Processing helix chain 'F' and resid 825 through 830 Processing sheet with id=AA1, first strand: chain 'B' and resid 76 through 79 removed outlier: 8.952A pdb=" N ALA B 109 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG B 39 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE B 111 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 41 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 113 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 43 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP B 115 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 110 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE B 146 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE B 112 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN B 148 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 114 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 143 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS B 218 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 145 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.176A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.852A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.177A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.439A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.559A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.663A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.076A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.821A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3166 1.34 - 1.46: 2366 1.46 - 1.58: 4406 1.58 - 1.70: 0 1.70 - 1.81: 102 Bond restraints: 10040 Sorted by residual: bond pdb=" N LEU F 642 " pdb=" CA LEU F 642 " ideal model delta sigma weight residual 1.462 1.494 -0.033 9.50e-03 1.11e+04 1.20e+01 bond pdb=" N ASP B 179 " pdb=" CA ASP B 179 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.77e+00 bond pdb=" N HIS F 641 " pdb=" CA HIS F 641 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 bond pdb=" N LEU F 639 " pdb=" CA LEU F 639 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.37e+00 bond pdb=" CA LEU F 642 " pdb=" C LEU F 642 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.17e-02 7.31e+03 5.21e+00 ... (remaining 10035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 13421 1.84 - 3.68: 171 3.68 - 5.53: 25 5.53 - 7.37: 8 7.37 - 9.21: 4 Bond angle restraints: 13629 Sorted by residual: angle pdb=" C LEU F 642 " pdb=" N PRO F 643 " pdb=" CA PRO F 643 " ideal model delta sigma weight residual 118.85 123.13 -4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" N PRO F 638 " pdb=" CA PRO F 638 " pdb=" C PRO F 638 " ideal model delta sigma weight residual 113.75 109.70 4.05 1.49e+00 4.50e-01 7.39e+00 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" N LEU F 642 " pdb=" CA LEU F 642 " pdb=" C LEU F 642 " ideal model delta sigma weight residual 113.25 110.05 3.20 1.30e+00 5.92e-01 6.04e+00 ... (remaining 13624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5010 17.19 - 34.38: 658 34.38 - 51.57: 245 51.57 - 68.77: 35 68.77 - 85.96: 10 Dihedral angle restraints: 5958 sinusoidal: 2312 harmonic: 3646 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -132.99 46.99 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " pdb=" OD1 ASP C 76 " ideal model delta sinusoidal sigma weight residual -30.00 -89.63 59.63 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG B 94 " pdb=" CD ARG B 94 " pdb=" NE ARG B 94 " pdb=" CZ ARG B 94 " ideal model delta sinusoidal sigma weight residual 180.00 135.01 44.99 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1172 0.043 - 0.086: 285 0.086 - 0.129: 97 0.129 - 0.172: 2 0.172 - 0.215: 2 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE F 773 " pdb=" CA ILE F 773 " pdb=" CG1 ILE F 773 " pdb=" CG2 ILE F 773 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL A 797 " pdb=" CA VAL A 797 " pdb=" CG1 VAL A 797 " pdb=" CG2 VAL A 797 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1555 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 775 " 0.012 2.00e-02 2.50e+03 1.35e-02 4.54e+00 pdb=" CG TRP F 775 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP F 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP F 775 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 775 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP F 775 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 596 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO F 597 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 597 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 597 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 196 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C THR C 196 " 0.027 2.00e-02 2.50e+03 pdb=" O THR C 196 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG C 197 " -0.009 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 14 2.63 - 3.20: 8704 3.20 - 3.76: 15489 3.76 - 4.33: 20813 4.33 - 4.90: 35147 Nonbonded interactions: 80167 Sorted by model distance: nonbonded pdb=" CG1 VAL A 627 " pdb=" CB ALA F 631 " model vdw 2.062 3.880 nonbonded pdb=" O LEU F 574 " pdb=" OG SER F 577 " model vdw 2.401 3.040 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.428 3.120 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.554 3.040 nonbonded pdb=" C THR F 736 " pdb=" OG1 THR F 736 " model vdw 2.561 2.616 ... (remaining 80162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 34.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10042 Z= 0.153 Angle : 0.561 9.212 13633 Z= 0.291 Chirality : 0.041 0.215 1558 Planarity : 0.004 0.041 1728 Dihedral : 17.713 85.957 3598 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 29.64 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1240 helix: 2.08 (0.22), residues: 584 sheet: -0.59 (0.35), residues: 216 loop : -0.36 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 775 HIS 0.008 0.001 HIS F 734 PHE 0.023 0.001 PHE A 761 TYR 0.013 0.001 TYR A 621 ARG 0.009 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.14424 ( 564) hydrogen bonds : angle 5.82996 ( 1635) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.55855 ( 4) covalent geometry : bond 0.00298 (10040) covalent geometry : angle 0.56063 (13629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7766 (mm-40) outliers start: 26 outliers final: 6 residues processed: 221 average time/residue: 1.4263 time to fit residues: 337.2761 Evaluate side-chains 112 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 110 optimal weight: 20.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** F 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.129747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078465 restraints weight = 22313.236| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.90 r_work: 0.3073 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10042 Z= 0.149 Angle : 0.665 12.922 13633 Z= 0.325 Chirality : 0.043 0.176 1558 Planarity : 0.004 0.036 1728 Dihedral : 5.707 128.679 1375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.63 % Allowed : 27.67 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1240 helix: 2.05 (0.22), residues: 581 sheet: -0.13 (0.35), residues: 208 loop : -0.43 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 100 HIS 0.008 0.001 HIS F 592 PHE 0.013 0.001 PHE F 730 TYR 0.020 0.001 TYR F 699 ARG 0.007 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 564) hydrogen bonds : angle 4.58060 ( 1635) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.86432 ( 4) covalent geometry : bond 0.00335 (10040) covalent geometry : angle 0.66491 (13629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8344 (tmm) REVERT: B 242 GLU cc_start: 0.9091 (tt0) cc_final: 0.8779 (tp30) REVERT: B 245 LYS cc_start: 0.9039 (mttp) cc_final: 0.8795 (mtmm) REVERT: C 172 GLU cc_start: 0.9208 (tp30) cc_final: 0.8946 (tp30) REVERT: C 214 ARG cc_start: 0.8674 (mmt-90) cc_final: 0.8276 (mpt180) REVERT: C 215 GLU cc_start: 0.8919 (mp0) cc_final: 0.8591 (mp0) REVERT: C 217 MET cc_start: 0.8435 (pmm) cc_final: 0.8130 (pmt) REVERT: D 21 MET cc_start: 0.8668 (tpp) cc_final: 0.8181 (tmm) REVERT: D 42 GLU cc_start: 0.8838 (pp20) cc_final: 0.8601 (pp20) REVERT: D 47 GLU cc_start: 0.8337 (mp0) cc_final: 0.8062 (mp0) REVERT: E 105 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7657 (ptt90) REVERT: A 577 PHE cc_start: 0.8758 (t80) cc_final: 0.8384 (m-80) REVERT: A 647 CYS cc_start: 0.8240 (m) cc_final: 0.7606 (p) REVERT: A 676 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7373 (mm-40) REVERT: A 682 MET cc_start: 0.7193 (mmp) cc_final: 0.6241 (ppp) REVERT: A 748 MET cc_start: 0.8821 (pmm) cc_final: 0.8458 (pmm) REVERT: A 836 MET cc_start: 0.8518 (ptp) cc_final: 0.8316 (ptp) REVERT: F 583 VAL cc_start: 0.5675 (OUTLIER) cc_final: 0.5372 (t) REVERT: F 621 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7287 (t) REVERT: F 649 SER cc_start: 0.6892 (OUTLIER) cc_final: 0.6583 (p) REVERT: F 689 MET cc_start: 0.7881 (mmm) cc_final: 0.7675 (mpm) REVERT: F 699 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6054 (p90) REVERT: F 816 LEU cc_start: 0.3931 (OUTLIER) cc_final: 0.3667 (pt) outliers start: 60 outliers final: 16 residues processed: 173 average time/residue: 1.2297 time to fit residues: 229.0090 Evaluate side-chains 133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 768 MET Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 40.0000 chunk 44 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** F 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.124347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071844 restraints weight = 22330.877| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.92 r_work: 0.2934 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 10042 Z= 0.231 Angle : 0.678 11.138 13633 Z= 0.331 Chirality : 0.044 0.187 1558 Planarity : 0.004 0.035 1728 Dihedral : 4.517 54.571 1368 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.53 % Allowed : 25.89 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1240 helix: 1.95 (0.21), residues: 575 sheet: -0.22 (0.35), residues: 217 loop : -0.43 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 698 HIS 0.009 0.001 HIS A 590 PHE 0.015 0.002 PHE C 235 TYR 0.021 0.002 TYR F 699 ARG 0.006 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 564) hydrogen bonds : angle 4.45608 ( 1635) SS BOND : bond 0.00873 ( 2) SS BOND : angle 1.51247 ( 4) covalent geometry : bond 0.00533 (10040) covalent geometry : angle 0.67775 (13629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLU cc_start: 0.9131 (tt0) cc_final: 0.8790 (tp30) REVERT: C 172 GLU cc_start: 0.9254 (tp30) cc_final: 0.8996 (tp30) REVERT: C 214 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8302 (mpt180) REVERT: C 215 GLU cc_start: 0.8911 (mp0) cc_final: 0.8451 (mp0) REVERT: C 217 MET cc_start: 0.8589 (pmm) cc_final: 0.8304 (pmt) REVERT: D 21 MET cc_start: 0.8771 (tpp) cc_final: 0.8551 (tpp) REVERT: E 89 GLU cc_start: 0.8776 (pm20) cc_final: 0.8560 (pm20) REVERT: E 105 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7574 (ptt180) REVERT: E 117 TYR cc_start: 0.8825 (m-80) cc_final: 0.8410 (m-80) REVERT: E 118 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.6741 (mtm-85) REVERT: A 577 PHE cc_start: 0.9013 (t80) cc_final: 0.8651 (m-80) REVERT: A 606 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6973 (pp) REVERT: A 612 LEU cc_start: 0.7850 (tp) cc_final: 0.7608 (mm) REVERT: A 676 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7420 (mm-40) REVERT: A 682 MET cc_start: 0.7101 (mmp) cc_final: 0.6185 (ppp) REVERT: A 748 MET cc_start: 0.8735 (pmm) cc_final: 0.8371 (pmm) REVERT: F 621 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (t) REVERT: F 689 MET cc_start: 0.8327 (mmm) cc_final: 0.8029 (mpm) REVERT: F 699 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6210 (p90) outliers start: 59 outliers final: 22 residues processed: 169 average time/residue: 1.1695 time to fit residues: 212.9293 Evaluate side-chains 139 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain F residue 768 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.124463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072426 restraints weight = 22150.703| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.96 r_work: 0.2946 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10042 Z= 0.155 Angle : 0.640 11.190 13633 Z= 0.307 Chirality : 0.042 0.192 1558 Planarity : 0.004 0.034 1728 Dihedral : 4.419 57.744 1368 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.85 % Allowed : 28.05 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1240 helix: 2.12 (0.22), residues: 576 sheet: -0.22 (0.36), residues: 205 loop : -0.40 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 698 HIS 0.010 0.001 HIS F 592 PHE 0.013 0.001 PHE B 232 TYR 0.022 0.001 TYR F 699 ARG 0.005 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 564) hydrogen bonds : angle 4.30940 ( 1635) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.97226 ( 4) covalent geometry : bond 0.00353 (10040) covalent geometry : angle 0.63950 (13629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLU cc_start: 0.9130 (tt0) cc_final: 0.8791 (tp30) REVERT: C 172 GLU cc_start: 0.9282 (tp30) cc_final: 0.9007 (tp30) REVERT: C 215 GLU cc_start: 0.8944 (mp0) cc_final: 0.8458 (mp0) REVERT: C 217 MET cc_start: 0.8641 (pmm) cc_final: 0.8336 (pmt) REVERT: C 339 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.7851 (m100) REVERT: D 21 MET cc_start: 0.8893 (tpp) cc_final: 0.8663 (tpp) REVERT: D 47 GLU cc_start: 0.8521 (mp0) cc_final: 0.8198 (mp0) REVERT: E 43 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8592 (mmmm) REVERT: E 89 GLU cc_start: 0.8689 (pm20) cc_final: 0.8447 (pm20) REVERT: E 105 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7535 (ptt180) REVERT: E 117 TYR cc_start: 0.8733 (m-80) cc_final: 0.8343 (m-80) REVERT: A 577 PHE cc_start: 0.9035 (t80) cc_final: 0.8740 (m-80) REVERT: A 612 LEU cc_start: 0.7893 (tp) cc_final: 0.7664 (mm) REVERT: A 676 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7525 (mm-40) REVERT: A 748 MET cc_start: 0.8648 (pmm) cc_final: 0.8240 (pmm) REVERT: F 621 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7644 (t) REVERT: F 689 MET cc_start: 0.8419 (mmm) cc_final: 0.8164 (mpm) outliers start: 41 outliers final: 24 residues processed: 149 average time/residue: 1.1508 time to fit residues: 185.1427 Evaluate side-chains 130 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 768 MET Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN E 35 ASN F 592 HIS ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.123156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071362 restraints weight = 22038.462| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.89 r_work: 0.2922 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10042 Z= 0.166 Angle : 0.621 12.505 13633 Z= 0.300 Chirality : 0.042 0.197 1558 Planarity : 0.004 0.035 1728 Dihedral : 4.380 58.482 1368 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.35 % Allowed : 26.64 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1240 helix: 2.09 (0.22), residues: 583 sheet: -0.17 (0.35), residues: 206 loop : -0.34 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 698 HIS 0.010 0.001 HIS F 592 PHE 0.011 0.001 PHE A 761 TYR 0.022 0.001 TYR F 699 ARG 0.004 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 564) hydrogen bonds : angle 4.24391 ( 1635) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.08117 ( 4) covalent geometry : bond 0.00382 (10040) covalent geometry : angle 0.62091 (13629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 242 GLU cc_start: 0.9149 (tt0) cc_final: 0.8819 (tp30) REVERT: C 172 GLU cc_start: 0.9284 (tp30) cc_final: 0.9010 (tp30) REVERT: C 215 GLU cc_start: 0.8936 (mp0) cc_final: 0.8424 (mp0) REVERT: C 217 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8292 (pmt) REVERT: D 21 MET cc_start: 0.9023 (tpp) cc_final: 0.8719 (tpp) REVERT: D 47 GLU cc_start: 0.8576 (mp0) cc_final: 0.8162 (mp0) REVERT: E 38 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7546 (ptp90) REVERT: E 89 GLU cc_start: 0.8723 (pm20) cc_final: 0.8416 (pm20) REVERT: E 105 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7578 (ptt180) REVERT: E 117 TYR cc_start: 0.8745 (m-80) cc_final: 0.8345 (m-80) REVERT: A 577 PHE cc_start: 0.9091 (t80) cc_final: 0.8812 (t80) REVERT: A 676 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 682 MET cc_start: 0.7068 (mmp) cc_final: 0.6405 (ppp) REVERT: A 748 MET cc_start: 0.8653 (pmm) cc_final: 0.8308 (pmm) REVERT: F 621 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7853 (t) REVERT: F 689 MET cc_start: 0.8490 (mmm) cc_final: 0.8186 (mpm) REVERT: F 775 TRP cc_start: 0.5539 (m100) cc_final: 0.5027 (m-90) outliers start: 57 outliers final: 27 residues processed: 155 average time/residue: 1.1961 time to fit residues: 200.0216 Evaluate side-chains 133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 768 MET Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071574 restraints weight = 22286.986| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.87 r_work: 0.2923 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10042 Z= 0.159 Angle : 0.646 14.165 13633 Z= 0.311 Chirality : 0.042 0.183 1558 Planarity : 0.004 0.042 1728 Dihedral : 4.330 58.495 1367 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.22 % Allowed : 27.67 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1240 helix: 2.00 (0.22), residues: 587 sheet: -0.17 (0.35), residues: 211 loop : -0.30 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 698 HIS 0.010 0.001 HIS F 592 PHE 0.012 0.001 PHE B 232 TYR 0.030 0.001 TYR A 769 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 564) hydrogen bonds : angle 4.18706 ( 1635) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.72214 ( 4) covalent geometry : bond 0.00366 (10040) covalent geometry : angle 0.64618 (13629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: C 172 GLU cc_start: 0.9286 (tp30) cc_final: 0.9012 (tp30) REVERT: C 215 GLU cc_start: 0.8938 (mp0) cc_final: 0.8416 (mp0) REVERT: C 217 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8304 (pmt) REVERT: C 339 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7832 (m100) REVERT: D 21 MET cc_start: 0.9083 (tpp) cc_final: 0.8749 (tpp) REVERT: D 47 GLU cc_start: 0.8623 (mp0) cc_final: 0.8233 (mp0) REVERT: E 38 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7549 (ptp90) REVERT: E 43 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8538 (mmmm) REVERT: E 89 GLU cc_start: 0.8738 (pm20) cc_final: 0.8320 (pm20) REVERT: E 117 TYR cc_start: 0.8768 (m-80) cc_final: 0.8288 (m-80) REVERT: A 577 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: A 676 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 682 MET cc_start: 0.7054 (mmp) cc_final: 0.6332 (ppp) REVERT: A 748 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8262 (pmm) REVERT: F 621 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7873 (t) REVERT: F 689 MET cc_start: 0.8553 (mmm) cc_final: 0.8267 (mpm) outliers start: 45 outliers final: 26 residues processed: 149 average time/residue: 1.1053 time to fit residues: 178.8893 Evaluate side-chains 139 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 768 MET Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.120404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068552 restraints weight = 22343.890| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.83 r_work: 0.2839 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10042 Z= 0.307 Angle : 0.725 14.079 13633 Z= 0.358 Chirality : 0.046 0.329 1558 Planarity : 0.004 0.043 1728 Dihedral : 4.572 56.960 1367 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.60 % Allowed : 28.14 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1240 helix: 1.83 (0.21), residues: 585 sheet: -0.15 (0.34), residues: 219 loop : -0.49 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 698 HIS 0.012 0.001 HIS F 592 PHE 0.032 0.002 PHE A 641 TYR 0.019 0.002 TYR F 699 ARG 0.013 0.001 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 564) hydrogen bonds : angle 4.43688 ( 1635) SS BOND : bond 0.00513 ( 2) SS BOND : angle 1.44507 ( 4) covalent geometry : bond 0.00710 (10040) covalent geometry : angle 0.72462 (13629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 1.192 Fit side-chains REVERT: B 242 GLU cc_start: 0.9279 (tt0) cc_final: 0.8878 (tp30) REVERT: C 172 GLU cc_start: 0.9302 (tp30) cc_final: 0.9051 (tp30) REVERT: C 215 GLU cc_start: 0.8887 (mp0) cc_final: 0.8353 (mp0) REVERT: C 217 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8354 (pmt) REVERT: D 47 GLU cc_start: 0.8717 (mp0) cc_final: 0.8287 (mp0) REVERT: E 38 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7573 (ptp90) REVERT: E 89 GLU cc_start: 0.9181 (pm20) cc_final: 0.8891 (pm20) REVERT: A 612 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 640 CYS cc_start: 0.8064 (t) cc_final: 0.7713 (m) REVERT: A 676 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7593 (mm-40) REVERT: A 682 MET cc_start: 0.7262 (mmp) cc_final: 0.6618 (ptm) REVERT: A 748 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (pmm) REVERT: F 621 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.8045 (t) REVERT: F 775 TRP cc_start: 0.5513 (m100) cc_final: 0.5025 (m-90) outliers start: 49 outliers final: 26 residues processed: 151 average time/residue: 1.1019 time to fit residues: 180.4025 Evaluate side-chains 135 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 chunk 106 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.122651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071517 restraints weight = 22230.794| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.75 r_work: 0.2901 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10042 Z= 0.151 Angle : 0.685 11.654 13633 Z= 0.330 Chirality : 0.043 0.196 1558 Planarity : 0.004 0.051 1728 Dihedral : 4.414 57.984 1367 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.75 % Allowed : 29.83 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1240 helix: 1.82 (0.22), residues: 590 sheet: -0.28 (0.35), residues: 211 loop : -0.43 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 698 HIS 0.012 0.001 HIS F 592 PHE 0.017 0.001 PHE B 232 TYR 0.018 0.001 TYR F 699 ARG 0.005 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 564) hydrogen bonds : angle 4.24528 ( 1635) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.44116 ( 4) covalent geometry : bond 0.00350 (10040) covalent geometry : angle 0.68547 (13629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.169 Fit side-chains REVERT: C 172 GLU cc_start: 0.9292 (tp30) cc_final: 0.9033 (tp30) REVERT: C 215 GLU cc_start: 0.8931 (mp0) cc_final: 0.8395 (mp0) REVERT: C 217 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8381 (pmt) REVERT: C 339 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.8001 (m100) REVERT: D 21 MET cc_start: 0.9164 (tpp) cc_final: 0.8687 (tmm) REVERT: D 47 GLU cc_start: 0.8680 (mp0) cc_final: 0.8374 (mp0) REVERT: E 38 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7513 (ptp90) REVERT: E 43 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8609 (mmmm) REVERT: E 89 GLU cc_start: 0.9143 (pm20) cc_final: 0.8856 (pm20) REVERT: E 117 TYR cc_start: 0.8815 (m-80) cc_final: 0.8385 (m-80) REVERT: A 676 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7544 (mm-40) REVERT: A 682 MET cc_start: 0.7260 (mmp) cc_final: 0.6683 (ptm) REVERT: A 690 MET cc_start: 0.7785 (tpt) cc_final: 0.7498 (tpt) REVERT: A 748 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8271 (pmm) REVERT: A 793 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8081 (tm) REVERT: F 621 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8209 (t) REVERT: F 689 MET cc_start: 0.9312 (tpp) cc_final: 0.8807 (mmp) REVERT: F 775 TRP cc_start: 0.5586 (OUTLIER) cc_final: 0.5048 (m-90) outliers start: 40 outliers final: 19 residues processed: 140 average time/residue: 1.1243 time to fit residues: 170.6403 Evaluate side-chains 132 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 775 TRP Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.121743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069751 restraints weight = 22077.154| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.86 r_work: 0.2883 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10042 Z= 0.142 Angle : 0.693 17.593 13633 Z= 0.331 Chirality : 0.042 0.170 1558 Planarity : 0.004 0.067 1728 Dihedral : 4.310 55.768 1367 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.00 % Allowed : 30.30 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1240 helix: 1.82 (0.22), residues: 592 sheet: -0.21 (0.34), residues: 220 loop : -0.40 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 698 HIS 0.012 0.001 HIS F 592 PHE 0.028 0.001 PHE A 770 TYR 0.018 0.001 TYR F 699 ARG 0.012 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 564) hydrogen bonds : angle 4.21972 ( 1635) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.45446 ( 4) covalent geometry : bond 0.00330 (10040) covalent geometry : angle 0.69328 (13629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.545 Fit side-chains REVERT: C 172 GLU cc_start: 0.9291 (tp30) cc_final: 0.9037 (tp30) REVERT: C 215 GLU cc_start: 0.8964 (mp0) cc_final: 0.8439 (mp0) REVERT: C 217 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8469 (pmt) REVERT: C 339 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.8093 (m100) REVERT: D 21 MET cc_start: 0.9178 (tpp) cc_final: 0.8696 (tmm) REVERT: D 47 GLU cc_start: 0.8730 (mp0) cc_final: 0.8440 (mp0) REVERT: E 43 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8633 (mmmm) REVERT: E 89 GLU cc_start: 0.9167 (pm20) cc_final: 0.8882 (pm20) REVERT: E 117 TYR cc_start: 0.8817 (m-80) cc_final: 0.8406 (m-80) REVERT: A 676 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7558 (mm-40) REVERT: A 690 MET cc_start: 0.7990 (tpt) cc_final: 0.7712 (tpt) REVERT: A 748 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8358 (pmm) REVERT: A 793 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8122 (tm) REVERT: F 621 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (t) REVERT: F 689 MET cc_start: 0.9369 (tpp) cc_final: 0.8903 (mmt) REVERT: F 775 TRP cc_start: 0.5655 (OUTLIER) cc_final: 0.5160 (m-90) outliers start: 32 outliers final: 17 residues processed: 134 average time/residue: 1.1515 time to fit residues: 167.2164 Evaluate side-chains 126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 775 TRP Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN F 592 HIS ** F 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.119106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067838 restraints weight = 21963.215| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.67 r_work: 0.2827 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10042 Z= 0.265 Angle : 0.744 13.368 13633 Z= 0.363 Chirality : 0.045 0.175 1558 Planarity : 0.005 0.066 1728 Dihedral : 4.536 59.663 1367 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.91 % Allowed : 30.77 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1240 helix: 1.79 (0.22), residues: 588 sheet: -0.22 (0.34), residues: 217 loop : -0.57 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 698 HIS 0.012 0.001 HIS F 592 PHE 0.032 0.002 PHE A 770 TYR 0.016 0.002 TYR F 699 ARG 0.011 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 564) hydrogen bonds : angle 4.35174 ( 1635) SS BOND : bond 0.00469 ( 2) SS BOND : angle 1.26511 ( 4) covalent geometry : bond 0.00619 (10040) covalent geometry : angle 0.74424 (13629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.182 Fit side-chains REVERT: C 172 GLU cc_start: 0.9294 (tp30) cc_final: 0.9054 (tp30) REVERT: C 215 GLU cc_start: 0.8911 (mp0) cc_final: 0.8431 (mp0) REVERT: C 217 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8424 (pmt) REVERT: D 21 MET cc_start: 0.9216 (tpp) cc_final: 0.8718 (tmm) REVERT: D 47 GLU cc_start: 0.8819 (mp0) cc_final: 0.8389 (mp0) REVERT: E 43 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8672 (mmmm) REVERT: E 89 GLU cc_start: 0.9171 (pm20) cc_final: 0.8880 (pm20) REVERT: A 676 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7688 (mm-40) REVERT: A 690 MET cc_start: 0.8223 (tpt) cc_final: 0.7947 (tpt) REVERT: A 748 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8404 (pmm) REVERT: A 814 MET cc_start: 0.7832 (mmt) cc_final: 0.7631 (mmt) REVERT: F 689 MET cc_start: 0.9329 (tpp) cc_final: 0.8851 (mmt) REVERT: F 775 TRP cc_start: 0.5570 (OUTLIER) cc_final: 0.5000 (m-90) outliers start: 31 outliers final: 20 residues processed: 124 average time/residue: 1.1707 time to fit residues: 157.4625 Evaluate side-chains 120 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain F residue 775 TRP Chi-restraints excluded: chain F residue 825 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 109 optimal weight: 40.0000 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 HIS ** F 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068615 restraints weight = 22015.001| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.79 r_work: 0.2861 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10042 Z= 0.152 Angle : 0.714 15.103 13633 Z= 0.342 Chirality : 0.043 0.169 1558 Planarity : 0.004 0.057 1728 Dihedral : 4.427 57.072 1367 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.16 % Allowed : 31.52 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1240 helix: 1.78 (0.22), residues: 592 sheet: -0.25 (0.34), residues: 220 loop : -0.48 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 698 HIS 0.012 0.001 HIS F 592 PHE 0.040 0.001 PHE A 779 TYR 0.017 0.001 TYR F 699 ARG 0.013 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 564) hydrogen bonds : angle 4.24665 ( 1635) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.56469 ( 4) covalent geometry : bond 0.00353 (10040) covalent geometry : angle 0.71443 (13629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9086.47 seconds wall clock time: 159 minutes 5.95 seconds (9545.95 seconds total)